Testing Evolution – Cost

There’s no end to the claims made for and about evolution and what evolution can allegedly accomplish without intelligent guidance. It seems as if Evolution ought to be treated as a god and capitalized. What would a true skeptic do without Evolution?

Far less common are actual metrics for testing evolutionary claims. For example, requests for how to write an actual test for claims about “the power of cumulative selection” are met with silence or scorn.

J.B.S Haldane once wrote:

A satisfactory theory of natural selection must be quantitative. In order to establish the view that natural selection is capable of accounting for the known facts of evolution we must show not only that it can cause a species to change, but that it can cause it to change at a rate which will account for present and past transmutations.

Was Haldane wrong? Did he expect too much from the theory?

Chase Nelson has a review essay article on Haldane’s Dilemma up over at Inference: International Review of Science.

What do readers think of his article? Is there a limit on the rate of evolution and why don’t claims for the alleged power of evolution include objective testing metrics such as calculations of cost?

71 thoughts on “Testing Evolution – Cost

  1. Tom English:
    Haldane’s Non-Dilemma,” by Ian Musgrave.

    Happy to see it basically reaffirms what I said earlier. There is no problem because the essay is based on a faulty rhetorical question.

    Oh but can it really be true that so few mutations separate us amazing super complex adaptive musician-mathematician humans versus that lowly, lowly, primitive and simple common ancestor we purportedly share with chimps?

    Yes. Yes it can.

  2. Rumraket

    Do you find this argument from the paper convincing?

    How many benefical mutations? While the majority of variation is neutral, the question remains exactly how much variation is due to selection, and does it break Haldane’s “speed limit”. Recent comparisons of Human and Chimp genomes, using the Macaque as an out group, have given us a good idea of how many genes have been fixed since the last common ancestor of chimps and humans (Bakewell, 2007).

    154

    Actually, that’s 154 of 13,888 genes. Given that we have around 22,000 genes [3] in our genome (http://www.ensembl.org/Homo_sapiens/index.html), then if the same percentage of beneficial mutations holds for the rest of the genome, no more than 238 fixed beneficial mutations is what separates us from the last common ancestor of chimps and humans.

    You are probably sitting there astonished that we are around 240 genes away from our last common ancestor with the chimp and saying “this can’t be right”[4] (how much did the guess you wrote down differ from the real thing?). However, this result agrees with previous estimates of the number of positively selected genes (Arbiza, 2006, Yu 2006). You can argue until the cows come home about whether you can get around Haldane’s assumptions using truncation selection, soft selection or whatever, the plain fact is that humans and the last common ancestor of humans and chimps are separated by far fewer fixed beneficial mutations than even Haldane’s limit allows.

  3. Tom English:
    Haldane’s Non-Dilemma,” by Ian Musgrave.

    I wish people could be consistent with the terms genes and alleles. I think I know the difference, and then I encounter writings by people who know more than I do, and who use the terms in ways that confuse me.

  4. colewd:
    Rumraket

    Do you find this argument from the paper convincing?

    The particular part you quoted only includes mutations in protein coding genes and doesn’t include regulatory sequences. I would include the mutations in regulatory regions, and then yes, I find it entirely convincing becuase it’s consistent with everything we know from developmental biology.

  5. Mung: Perhaps Joe will weigh in and explain why cost is a problem and why it is taken seriously.

    I have been at scientific meetings and am on my way home today. Will weigh in after that, having by then had a chance to read Chase Nelson’s article.

  6. Rumraket,

    Actually, that’s 154 of 13,888 genes. Given that we have around 22,000 genes [3] in our genome (http://www.ensembl.org/Homo_sapiens/index.html), then if the same percentage of beneficial mutations holds for the rest of the genome, no more than 238 fixed beneficial mutations is what separates us from the last common ancestor of chimps and humans.

    I agree on missing regulatory data. In his conclusion above he seems to be conflating genes with mutations or claiming that new genes only came from a single mutation.

  7. petrushka: Tom English:
    “Haldane’s Non-Dilemma,” by Ian Musgrave.

    I wish people could be consistent with the terms genes and alleles. I think I know the difference, and then I encounter writings by people who know more than I do, and who use the terms in ways that confuse me

    Yeah it’s quite confusing how he goes back and forth but if you just take it to mean gene it makes sense throughout.

  8. colewd: I agree on missing regulatory data. In his conclusion above he seems to be conflating genes with mutations or claiming that new genes only came from a single mutation.

    He doesn’t use the term allele which he should be doing. That’s what he means. They are genes with mutations in them, being fixed.

  9. petrushka: I wish people could be consistent with the terms genes and alleles. I think I know the difference, and then I encounter writings by people who know more than I do, and who use the terms in ways that confuse me.

    I see now that Ian got careless toward the end. I see also that Haldane used gene where I would expect allele. “If gold rust, what then will iron do?”

  10. I think people who know biology well just filter out the inconsistency, but for someone trying to learn, it’s confusing.

  11. Joe, if and when you manage to get to it, could you explain what the relationship is between cost and the speed of evolution and what the fossil record can tell us about either?

    Because my position is that cost isn’t about speed and fossils are irrelevant. And I’d sure like to hear why I am wrong and all these other commenters here at TSZ are right.

    My understanding is that cost is about how many offspring have to be produced relative to the alternatives. A single mutation in a population must be favored in such a way as to be able to replace the original type. These requires a reproductive excess. It is this excess which is “the cost.”

  12. Mung, I have now read the article. I am somewhat confused as to what Nelson’s argument is, in spite of all the references and all the detail. He mentions Walter ReMine’s argument from reproductive excess. But Nelson does not firmly back that as the Cost. (Nelson also mentions my name there, but does not show any sign of having read my 1971 paper, which he does not list in his references. My argument in the 1971 paper is very different from Crow’s and from ReMine’s. Nelson seems to think that Crow and I were calculating the same thing.)

    There is the issue of whether the Cost is something that is bad for the species, so that with too much Cost it goes extinct, or whether it is bad for our scenario, so that too high a cost means that things could not have happened that way. The cost that I was calculating in 1971 was the former. I concluded, for example, that beneficial substitutions incurred no cost, as they raise the reproductive excess.

    In my 1971 paper I imagined a species with one substitution starting every k generations, with all these substitutions being responses to a deteriorating environment, and the allele that starts substituting being able to counteract the effect of that deterioration. The Cost was the reproductive excess necessary to avoid extinction. It comes out close to, but not exactly the same as, Haldane’s calculation.

    ReMine’s “cost” is of the latter sort. It is incurred whether the substitution is a response to environmental deterioration or is simply a new beneficial mutation. It is measured in reproductive excess, required to explain the observed gene frequency changes. One issue is how one combines Cost from two or more substitutions. That is unclear from ReMine’s article. If you want to discuss that article, fine.

  13. Joe Felsenstein: Nelson seems to think that Crow and I were calculating the same thing.

    Hi Joe,

    So Nelson does not include your 1971 paper in his list of references, and it appears to you as if he hasn’t read it. I can certainly help ameliorate that situation. Can you provide a link to your paper?

    It still seems to be an open question however of what ‘cost’ means. You appear to adopt the ‘reproductive excess’ version.

    What’s the relevance of the fossil record?

    What’s the relevance to the speed of evolution?

    Can you help clear up some of the fog surrounding Haldane’s Dilemma?

  14. phoodoo: Its bizarre that evolutionists can take virtually any data and claim that it supports their theory.

    Not bizarre at all. Commonplace.

  15. Mung: Not bizarre at all. Commonplace.

    So long as we redefine supporting data as “virtually any”, it’s commonplace. But on the other hand, ALL observations support ID. The exact opposite of all such observations would ALSO support ID.

  16. Flint: So long as we redefine supporting data as “virtually any”, it’s commonplace. But on the other hand, ALL observations support ID. The exact opposite of all such observations would ALSO support ID.

    Heh, reminds me of Durstons origin of life “calculations”. If life originated more than once, then it’s doubly miraculous! LOL

  17. Mung: So Nelson does not include your 1971 paper in his list of references, and it appears to you as if he hasn’t read it. I can certainly help ameliorate that situation. Can you provide a link to your paper?

    No, because it is behind a firewall and I am not able to post a link to a free version. It will be found in JSTOR (and Nelson can see it there if he has access to a JSTOR account or is willing to pay their fee). It is in American Naturalist, volume 105, issue 1, pages 1-11, 1971.

    It still seems to be an open question however of what ‘cost’ means. You appear to adopt the ‘reproductive excess’ version.

    It is absolutely correct that the meaning of “cost” is unclear. My argument there is that if one takes the cost to be reduction of fitness due to continual environmental changes, and if there are alleles around that counteract each of these changes, then one can calculate a meaningful “cost” as the reproductive excess necessary to avoid extinction.

    Others, however, have different concepts of what ‘”cost” is and what is the consequence of too high a cost. Nelson’s article does not (to me, anyway) clarify all this. He treats very different notions of “cost”, such as mine and ReMine’s, as equivalent.

    If he wants to come here and discuss this, he would of course be welcome.

    What’s the relevance of the fossil record?

    Not clear there is any, in this discussion. But of course very important to evolutionary biology generally.

    What’s the relevance to the speed of evolution?

    If all the substitutions are selective responses to deteriorations of the environment, then my calculations are relevant to the total rate of those substitutions. If …

    Can you help clear up some of the fog surrounding Haldane’s Dilemma?

    Well, if we argue that Haldane’s Dilemma is that if deteriorations of the environment impose too much reduction in fitness, and there is not enough response to natural selection to counteract that, then my calculations are precisely relevant.

    But if you just say that there are too many substitutions, so that the “cost” is too high, then you had better make clear(er) what you mean by “cost”.

  18. Mung,

    Not bizarre at all. Commonplace.

    Then give examples of such inappropriate use of evidence. Name names and back up your claim!

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